Merge pull request #115 from MaxUlysse/Abstract

Add abstract

CHANGELOG.md

@@ -10,6 +10,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 
 - [#76](https://github.com/nf-core/sarek/pull/76) - Add `GATK Spark` possibilities to Sarek
 - [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report
+- [#115](https://github.com/nf-core/sarek/pull/115) - Add [@szilvajuhos](https://github.com/szilvajuhos) abstract for ESHG2020
 
 ### `Changed`
 

docs/abstracts/2020-06-ESHG.md

@@ -0,0 +1,39 @@
+# European Society of Human Genetics - European Human Genetics Conference - Berlin, Germany, 2020-06
+
+## Reproduce easily: analysis of matching tumor-normal NGS data with the Sarek workflow
+
+Szilveszter Juhos,
+Maxime Garcia,
+Teresita Díaz de Ståhl,
+Markus Mayrhofer,
+Johanna Sandgren,
+Monica Nistér
+
+### Introduction
+
+High throughput sequencing for precision medicine is now a routine method.
+Numerous tools have to be used, and analysis is time consuming.
+We propose Sarek, an open-source container based bioinformatics workflow for germline or matching tumor-normal pairs, written in Nextflow, to process WGS, whole-exome or gene-panel samples.
+
+#### Materials and methods
+
+Sarek is part of nf-core, a collection of peer-reviewed workflows; supported environments are Conda, Docker and Singularity.
+It is system-agnostic: can be used on single machines, clusters (HPC) or in a cloud such as AWS, with little difference between setups.
+Additional software can be included as new modules.
+Several model organism references are available (including Human GRCh37 and GRCh38).
+The pipeline reports germline and somatic SNVs and SVs (by HaplotypeCaller, Strelka, Mutect2, Manta and TIDDIT).
+CNVs, purity and ploidy is estimated by ASCAT and Control-FREEC.
+Furthermore, a broad set of QC metrics is reported at the end of the workflow with MultiQC.
+
+#### Results
+
+From FASTQs to annotated VCFs it takes three days for a 90X/90X sample on a 48 cores node.
+Sarek is used in production at the National Genomics Infrastructure Sweden for germline and cancer samples for the Swedish Childhood Tumor Biobank and other research groups.
+
+#### Conclusions
+
+Sarek is an easy-to-use tool for germline or cancer NGS samples, to be downloaded from [nf-co.re/sarek](https://nf-co.re/sarek) under MIT license.
+
+#### Supporting grants
+
+Swedish Research Council (2017-00630, 2017-00656), the Swedish Childhood Cancer Fund (BTB: BB2017-0001; BB2018-0001; BB2019-0001), and the Knut and Alice Wallenberg Foundation (KAW 2014.0278).